It also revealed high levels of dissatisfaction with the way street fundraising by so-called 'chuggers' is conducted, although 22pc understood charities need to pursue all funding options.
Some 37pc said being approached at their doorstep for funding was inappropriate.
The survey was carried out in advance of a new set of fundraising guidelines for charities from the regulator, which put the onus on collectors to respect donors and operate with integrity and honesty.
Mr Farrelly said he believed the guidelines were proportionate and fair.
"We will require the trustees of each registered charity to be able to explain and justify their approach to fundraising, particularly if they decide not to follow good practice," he told a gathering of charity officials in Dublin.
Rural and Community Development Minister Michael Ring, who launched the guidelines, said better regulation would help "get rid of the rogues that caused the problems in relation to charities in this country".
He added: "I won't speak on any individual case but we were all disappointed with what we saw happening over the last number of years."
He will bring forward regulation next year which will force charities to be financially transparent in their annual accounts, revealing salaries of executives and other information.
The consultation by the Charities Regulator found the biggest concern among donors is the potential misuse of funds.
One-third worry about how funds will be spent. Just 1pc say they never give to charity.
Irish Independent online